However, once I have it uploaded I am having trouble embedding it into a project at a specific size. I have tried multiple plug-ins but most don't work in any browser. Top Flash Embed was the only one I found that was compatable with 3.6.1 but development has stopped and I'm having sizing and cross platform issues with it.

Common php best practice is to not include the closing "?>" php tag if it's the last line in the file. Just put the code above at the bottom of functions.php. (actually, it can go anywhere in the file.)